Vandana Kukshal wrote:
> hello sir ,
>
> recently i have collected one data of 3.0 A of a protein having no
> sequence homology with any known PDB .
> but
> while fold prediction i got 100 % identical fold with some of the
> protein .
> space group of my protein is P622 and showing 6 molecule in a
> assymetric unit.
> the homologous fold proteins are trimer protein.
> can i run MR in this case . how i should proceed.
> i m trying for MIR also .
> regards
> vandana
I suggest that you ccp4i, then phaser within ccp4i (or Alexeai Vaguin's
program, Molrep i think it's called). The "easiest" and perhaps most
clever approach would be to give as a search model the trimer, and look
for 2 copies in the asymmetric unit. Otherwise (if your protein does not
assemble as trimers, for example as a dimer of trimers) then you give as
a search model a single monomer, and look for 6 copies. But this can be
tricky.
You may have to edit your search model before. In any case, you should
always remove the waters present in the pdb of your search model.
HTH,
Fred.
PS how do you know you have 6 molecules in the asymmetric unit?